Hello SEQanswers
My name is Kurt Lamour and I run a company (Floodlight Genomics) that provides a new low cost option for targeted genetic sequencing (MonsterPlex). MonsterPlex is a single-tube PCR-based technology to amplify 10's to 100's of targets from small amounts DNA (e.g. 20-40ng). Custom indices are added during the multiplex PCR and we currently index up to 6000 samples for pooling (loaded as a single library) on an Illumina or Ion device.

Total target sizes can be either 80, 380 or 480bp. It depends on your goals and/or the sequencing device and configuration you'd like to use.

I'm an academic research scientist (molecular epidemiologist) who developed MonsterPlex to better use the huge amount of excess sequence data our lab was producing using WGS and GBS. Thus far we've worked directly with academic research scientists on native grasses, insects, infected plants and large mammals. Any target is fair game!

Best I can tell, our project costs are low. For example, the cost to analyze 1000 samples for 100 targets (=100,000 data points) is less than $0.10/target at >20X coverage per target. You provide the DNA and the target sequences and we deliver the sample-specific sequence data. MonsterPlex should work equally well on cDNA, making for some interesting RNAseq options - although I've yet to try it.